[2024-01-24 13:32:41,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference
[2024-01-24 13:32:42,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,508] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,508] [INFO] Running command: gunzip -c /var/lib/cwl/stge83804b6-56e8-4b72-9ae5-e21d18bbd69f/GCF_025146565.1_ASM2514656v1_genomic.fna.gz | prodigal -d GCF_025146565.1_ASM2514656v1_genomic.fna/cds.fna -a GCF_025146565.1_ASM2514656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:01,464] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:01,464] [INFO] Task started: HMMsearch
[2024-01-24 13:33:01,465] [INFO] Running command: hmmsearch --tblout GCF_025146565.1_ASM2514656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference/reference_markers.hmm GCF_025146565.1_ASM2514656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:01,820] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:01,821] [INFO] Found 6/6 markers.
[2024-01-24 13:33:01,856] [INFO] Query marker FASTA was written to GCF_025146565.1_ASM2514656v1_genomic.fna/markers.fasta
[2024-01-24 13:33:01,857] [INFO] Task started: Blastn
[2024-01-24 13:33:01,857] [INFO] Running command: blastn -query GCF_025146565.1_ASM2514656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference/reference_markers.fasta -out GCF_025146565.1_ASM2514656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:02,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:02,481] [INFO] Selected 9 target genomes.
[2024-01-24 13:33:02,481] [INFO] Target genome list was writen to GCF_025146565.1_ASM2514656v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:02,484] [INFO] Task started: fastANI
[2024-01-24 13:33:02,484] [INFO] Running command: fastANI --query /var/lib/cwl/stge83804b6-56e8-4b72-9ae5-e21d18bbd69f/GCF_025146565.1_ASM2514656v1_genomic.fna.gz --refList GCF_025146565.1_ASM2514656v1_genomic.fna/target_genomes.txt --output GCF_025146565.1_ASM2514656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,266] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:11,266] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:11,266] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	100.0	1402	1402	95	conclusive
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	99.9953	1401	1402	95	conclusive
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	99.9464	1386	1402	95	conclusive
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	85.1628	790	1402	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	85.1451	786	1402	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	85.0568	862	1402	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	84.8493	810	1402	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	80.1103	466	1402	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	80.0954	489	1402	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,267] [INFO] DFAST Taxonomy check result was written to GCF_025146565.1_ASM2514656v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:11,268] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:11,268] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:11,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference/checkm_data
[2024-01-24 13:33:11,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:11,309] [INFO] Task started: CheckM
[2024-01-24 13:33:11,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025146565.1_ASM2514656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025146565.1_ASM2514656v1_genomic.fna/checkm_input GCF_025146565.1_ASM2514656v1_genomic.fna/checkm_result
[2024-01-24 13:34:03,428] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:03,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:03,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:03,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:03,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025146565.1_ASM2514656v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:03,445] [INFO] Task started: Blastn
[2024-01-24 13:34:03,445] [INFO] Running command: blastn -query GCF_025146565.1_ASM2514656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffbc5d91-dac7-454f-a764-e7d0e86b36d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025146565.1_ASM2514656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:04,282] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:04,285] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:04,285] [INFO] Target genome list was writen to GCF_025146565.1_ASM2514656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:04,291] [INFO] Task started: fastANI
[2024-01-24 13:34:04,291] [INFO] Running command: fastANI --query /var/lib/cwl/stge83804b6-56e8-4b72-9ae5-e21d18bbd69f/GCF_025146565.1_ASM2514656v1_genomic.fna.gz --refList GCF_025146565.1_ASM2514656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025146565.1_ASM2514656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:12,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:12,517] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:12,517] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000155815.1	s__Bacteroides eggerthii	99.9464	1386	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	conclusive
GCF_900129655.1	s__Bacteroides clarus	85.1495	786	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_003438615.1	s__Bacteroides sp003545565	85.0936	838	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000154525.1	s__Bacteroides stercoris	84.8052	801	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000374365.1	s__Bacteroides gallinarum	82.8942	757	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_910578895.1	s__Bacteroides sp910578895	82.4613	643	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	80.386	529	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_007896885.1	s__Bacteroides sp007896885	77.4105	149	1402	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.28	98.56	0.94	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:12,518] [INFO] GTDB search result was written to GCF_025146565.1_ASM2514656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:12,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:12,521] [INFO] DFAST_QC result json was written to GCF_025146565.1_ASM2514656v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:12,521] [INFO] DFAST_QC completed!
[2024-01-24 13:34:12,521] [INFO] Total running time: 0h1m31s